Defining Small Intestinal Bacterial Overgrowth by Culture and High Throughput Sequencing

Gabriela Leite; Ali Rezaie; Ruchi Mathur; Gillian M Barlow; Mohamad Rashid; Ava Hosseini; Jiajing Wang; Gonzalo Parodi; Maria Jesus Villanueva-Millan; Maritza Sanchez; Walter Morales; Stacy Weitsman; Mark Pimentel; REIMAGINE Study Group

doi:10.1016/j.cgh.2023.06.001

Defining Small Intestinal Bacterial Overgrowth by Culture and High Throughput Sequencing

Clin Gastroenterol Hepatol. 2024 Feb;22(2):259-270. doi: 10.1016/j.cgh.2023.06.001. Epub 2023 Jun 12.

Collaborators

Affiliations

¹ Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California.
² Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California; Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai, Los Angeles, California.
³ Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California; Division of Endocrinology, Diabetes, and Metabolism, Cedars-Sinai, Los Angeles, California.
⁴ Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California; Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai, Los Angeles, California. Electronic address: mark.pimentel@cshs.org.

PMID: 37315761
DOI: 10.1016/j.cgh.2023.06.001

Abstract

Background& aims: Despite accelerated research in small intestinal bacterial overgrowth (SIBO), questions remain regarding optimal diagnostic approaches and definitions. Here, we aim to define SIBO using small bowel culture and sequencing, identifying specific contributory microbes, in the context of gastrointestinal symptoms.

Methods: Subjects undergoing esophagogastroduodenoscopy (without colonoscopy) were recruited and completed symptom severity questionnaires. Duodenal aspirates were plated on MacConkey and blood agar. Aspirate DNA was analyzed by 16S ribosomal RNA and shotgun sequencing. Microbial network connectivity for different SIBO thresholds and predicted microbial metabolic functions were also assessed.

Results: A total of 385 subjects with <10³ colony forming units (CFU)/mL on MacConkey agar and 98 subjects with ≥10³ CFU/mL, including ≥10³ to <10⁵ CFU/mL (N = 66) and ≥10⁵ CFU/mL (N = 32), were identified. Duodenal microbial α-diversity progressively decreased, and relative abundance of Escherichia/Shigella and Klebsiella increased, in subjects with ≥10³ to <10⁵ CFU/mL and ≥10⁵ CFU/mL. Microbial network connectivity also progressively decreased in these subjects, driven by the increased relative abundance of Escherichia (P < .0001) and Klebsiella (P = .0018). Microbial metabolic pathways for carbohydrate fermentation, hydrogen production, and hydrogen sulfide production were enhanced in subjects with ≥10³ CFU/mL and correlated with symptoms. Shotgun sequencing (N = 38) identified 2 main Escherichia coli strains and 2 Klebsiella species representing 40.24% of all duodenal bacteria in subjects with ≥10³ CFU/mL.

Conclusions: Our findings confirm ≥10³ CFU/mL is the optimal SIBO threshold, associated with gastrointestinal symptoms, significantly decreased microbial diversity, and network disruption. Microbial hydrogen- and hydrogen sulfide-related pathways were enhanced in SIBO subjects, supporting past studies. Remarkably few specific E coli and Klebsiella strains/species appear to dominate the microbiome in SIBO, and correlate with abdominal pain, diarrhea, and bloating severities.

Keywords: Escherichia; Klebsiella; Metabolic Pathways; Small Intestinal Bacterial Overgrowth; Small Intestinal Microbiome.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Agar
Breath Tests
Escherichia coli
Gastrointestinal Diseases*
High-Throughput Nucleotide Sequencing
Humans
Hydrogen
Hydrogen Sulfide*

Substances

Agar
Hydrogen Sulfide
Hydrogen